Fluorescent sensor for redox environment: a redox controlled molecular device based on the reversible mercury mediated folded structure formation of oligothymidylate

Enzymatic formation of consecutive thymine–HgII–thymine base pairs by DNA polymerases

Ten consecutive T–Hg^II–T base pairs were successfully formed by DNA polymerase-catalyzed primer extension reactions.

Potentiometric aptasensing based on target-induced conformational switch of a DNA probe using a polymeric membrane silver ion-selective electrode

In this article, we introduce a general, sensitive, facile, and label-free potentiometric assay based on metal-mediated DNA base pairs. A nucleic acid with one adenosine-5'-triphosphate (ATP) binding sequence (aptamer) in the middle and two cytosine(C)-rich sequences at the lateral portions was employed as a model. A rigid hairpin structure can be formed in the presence of Ag(+) ions, in which the C residues of the spatially separated nucleotides are linked by the ions. The strong interaction between Ag(+) ions and cytosines forms a stable C-Ag(+)-C structure, which could reduce the concentration of silver ions released from the polymeric membrane silver ion-selective electrode (ISE) at the sample-membrane interface and decrease the potential response. In the presence of its target, the aptamer (the loop sequence of the probe) binds specifically to the target via reaction incubation. Such target-binding induced aptamer conformational change prevents the formation of C-Ag(+)-C structure, leaving more silver ions at the sample-membrane interface, which can be detected by the silver ISE. ATP can be quantified in the range of 0.5-3.0 μM with a detection limit of 0.37 μM. The relative standard deviation for 5 μM ATP is 5.5%. For the proposed method, the combination of using ion fluxes of silver ions as modulating reagents and as signal reporters greatly simplifies the detection procedures. In addition, by changing the binding sequence in the middle of the probe, the present detection method will be able to explore new applications of ISE for the detection of a large variety of targets.

Raman spectroscopic detection of the T-Hg II-T base pair and the ionic characteristics of mercury

Developing applications for metal-mediated base pairs (metallo-base-pair) has recently become a high-priority area in nucleic acid research, and physicochemical analyses are important for designing and fine-tuning molecular devices using metallo-base-pairs. In this study, we characterized the Hg(II)-mediated T-T (T-Hg(II)-T) base pair by Raman spectroscopy, which revealed the unique physical and chemical properties of Hg(II). A characteristic Raman marker band at 1586 cm(-1) was observed and assigned to the C4=O4 stretching mode. We confirmed the assignment by the isotopic shift ((18)O-labeling at O4) and density functional theory (DFT) calculations. The unusually low wavenumber of the C4=O4 stretching suggested that the bond order of the C4=O4 bond reduced from its canonical value. This reduction of the bond order can be explained if the enolate-like structure (N3=C4-O4(-)) is involved as a resonance contributor in the thymine ring of the T-Hg(II)-T pair. This resonance includes the N-Hg(II)-bonded state (Hg(II)-N3-C4=O4) and the N-Hg(II)-dissociated state (Hg(II+) N3=C4-O4(-)), and the latter contributor reduced the bond order of N-Hg(II). Consequently, the Hg(II) nucleus in the T-Hg(II)-T pair exhibited a cationic character. Natural bond orbital (NBO) analysis supports the interpretations of the Raman experiments.

Metal-mediated base pairs in nucleic acids with purine- and pyrimidine-derived nucleosides

Metal-mediated base pairs are transition metal complexes formed from complementary nucleosides within nucleic acid double helices. Instead of relying on hydrogen bonds, they are stabilized by coordinative bonds. The nucleosides acting as ligands do not necessarily have to be artificial. In fact, several examples are known of naturally occurring nucleobases (e.g., thymine, cytosine) capable of forming stable metal-mediated base pairs that are highly selective towards certain metal ions. This chapter provides a comprehensive overview of metal-mediated base pairs formed from natural nucleosides or from closely related artificial nucleosides that are pyrimidine or purine derivatives. It addresses the different strategies that lead to the development of these base pairs. The article focuses on structural models for metal-mediated base pairs, their experimental characterization within a nucleic acid, and on their possible applications.

Interaction of inorganic mercury with CoA-SH and acyl-CoAs

Sulfur containing biomolecules are involved in complexes with mercury. CoA is an important cofactor for many enzymes involved in metabolic processes. Fatty acyl-CoA-thioesters, substrates of mitochondrial ß-oxidation, are sulfur containing compounds and potential mercury ligands. The CoA-Hg(2+) complex can be easily assessed by UV-Vis spectroscopy or indirectly by antibacterial tests that reconfirmed the protective role of CoA on E. coli. The characteristics of these complexes were determined by means of FTIR spectroscopy. The reverse phase liquid chromatography combined with electrospray ionization tandem mass spectrometry was used for detection of the side-product that resulted through the cleavage of thioesters in the presence of mercury. An unexpected result was the detection of octathioic acid as a product. Our study shows that mitochondrial β-oxidation can be affected by thioesters depletion assisted by Hg(2+). The GC-MS technique could be used to detect some possible mitochondrial injuries due to the heavy metal ions.

Silver ions-mediated conformational switch: facile design of structure-controllable nucleic acid probes

Conformationally constraint nucleic acid probes were usually designed by forming an intramolecular duplex based on Watson-Crick hydrogen bonds. The disadvantages of these approaches are the inflexibility and instability in complex environment of the Watson-Crick-based duplex. We report that this hydrogen bonding pattern can be replaced by metal-ligation between specific metal ions and the natural bases. To demonstrate the feasibility of this principle, two linear oligonucleotides and silver ions were examined as models for DNA hybridization assay and adenosine triphosphate detection. The both nucleic acids contain target binding sequences in the middle and cytosine (C)-rich sequences at the lateral portions. The strong interaction between Ag(+) ions and cytosines forms stable C-Ag(+)-C structures, which promises the oligonucleotides to form conformationally constraint formations. In the presence of its target, interaction between the loop sequences and the target unfolds the C-Ag(+)-C structures, and the corresponding probes unfolding can be detected by a change in their fluorescence emission. We discuss the thermodynamic and kinetic opportunities that are provided by using Ag(+) ion complexes instead of traditional Watson-Crick-based duplex. In particular, the intrinsic feature of the metal-ligation motif facilitates the design of functional nucleic acids probes by independently varying the concentration of Ag(+) ions in the medium.

Highly sensitive fluorescent sensor for mercury ion based on photoinduced charge transfer between fluorophore and pi-stacked T-Hg(II)-T base pairs

A novel and simple oligodeoxyribonucleotide-based sensor with single fluorophore-labeled for mercury ion sensing was reported. An oligodeoxyribonucleotide poly(dT) was labeled with fluorescein as donor. Based on the specific binding of Hg(II) to T-T mismatch base pairs, the formation of pi-stacked [T-Hg(II)-T] with "sandwich" structure on the addition of Hg(II) ions facilitates the electron transfer via photoinduced charge transfer (PCT), which creates an additional nonradiative decay channel for excited fluorophore and triggers the fluorescence to be quenched. The pi-stacked [T-Hg(II)-T] functioned not only as mercury ion recognition but also as an electron acceptor to quench the donor. A linear relationship was observed over the range of 0-1.0 microM with the detection limit of 20 nM for mercury ions. The fluorescence quenching phenomenon and quenching mechanism, reliability and selectivity of the system were investigated in detail.

Detection of mercury(II) based on Hg2+ -DNA complexes inducing the aggregation of gold nanoparticles

A DNA-Au NP probe for sensing Hg2+ using the formation of DNA-Hg2+ complexes through thymidine (T)-Hg2+ -T coordination to control the negative charge density of the DNA strands-thereby varying their structures-adsorbed onto Au NPs.

Using in vitro transcription to construct scaffolds for one-dimensional arrays of mercuric ions

In vitro transcription by T7 RNA polymerase can be used to construct scaffolds for the one-dimensional arrangement of mercury(II) ions. In these constructs, the metal ions are located inside of RNA double helices. By replacing the amide protons of two oppositely located uracil residues of complementary strands, mercury(II) becomes coordinated in a linear fashion to form metal-ion mediated base pairs, analogous to the well-known thymine-Hg-thymine base pair in DNA. This is shown here by a combination of various experimental techniques, including NMR spectroscopy, dynamic light scattering, as well as UV and CD spectroscopy. A total of five different double helices, including both palindromic and non-palindromic RNA sequences and between two and twenty consecutive uracil residues, have been synthesized and shown to be able to incorporate mercury(II). The synthesis of r(GGAGU 20CUCC) demonstrates that T7 polymerase is capable of handling long continuous stretches of identical nucleotides, albeit at the cost of an increasing number of abortion products and longer oligonucleotide strands that need to be separated by polyacrylamide gel electrophoresis. This work introduces RNA into the group of nucleic acids that can form metal ion mediated base pairs. The use of such metal-modified nucleic acids has been envisaged in various fields of research, including the generation of molecular wires.

Conformational change induced by metal-ion-binding to DNA containing the artificial 1,2,4-triazole nucleoside

A conformational switch can be induced upon the addition of transition-metal ions to oligonucleotides that contain a row of successive artificial nucleobases flanked by complementary sequences of natural nucleobases, provided that the artificial bases cannot undergo self-pairing via hydrogen bonding but only via the formation of metal-ion-mediated base pairs. Such oligonucleotides adopt a hairpin structure in the absence of transition-metal ions, yet they show a preference for the formation of a regular double helix if the appropriate metal ions are present. We report here our experimental data on the structure of the oligonucleotide d(A7X3T7) (A=adenine, T=thymine, X=1,2,4-triazole) in the absence and presence of silver(I). This study comprising temperature-dependent UV spectroscopy, CD spectroscopy, MALDI-TOF measurements, fluorescence spectroscopy, and dynamic light scattering opens up a new approach to the generation of a large variety of metal-ion sensors with the possibility of fine-tuning their sensing capabilities, depending on the artificial nucleoside that is used.

Differential reactivity of α and β 2′-deoxyribonucleosides towards protonation and metalation

The reactivity of artificial 2'-deoxyribonucleosides, designed as nucleoside surrogates in metal-mediated base pairs, towards protonation and metalation has been shown to be dependent on the choice of the anomer. The alpha nucleosides comprising the aglycones imidazole, 1,2,4-triazole, benzimidazole and imidazo[4,5-b]pyridine are more basic than the respective beta nucleosides as was shown by a combined experimental and theoretical approach. The DeltapK(a) values observed experimentally are in the range of 0.19+/-0.03 to 0.41+/-0.07 (with the error representing three times the standard deviation of the mean value). An independent confirmation of this differential reactivity was obtained from density functional theory (DFT) calculations using 1,2,4-triazole nucleoside as an example. The result of these calculations is in good agreement with the experimental data (DeltapK(a)=0.16 vs. 0.21+/-0.07). The stability of the respective metal ion complexes of the anomeric 1,2,4-triazole nucleosides follows the same trend as that of the respective protonated nucleosides: Those of the alpha nucleoside are more stable than those of the beta nucleoside (Deltalogbeta(2)=0.6+/-0.2 for the 2:1 complex with Ag(+); Deltalogbeta(1)=0.51+/-0.07 for the 1:1 complex with Hg(2+)). These slightly different reactivities will be useful for fine-tuning the metal-ion binding behavior of oligonucleotides containing metal-mediated base pairs.

Highly Selective Chromogenic and Redox or Fluorescent Sensors of Hg2+in Aqueous Environment Based on 1,4-Disubstituted Azines

Two new chemosensors that exhibit high affinity and high selectivity for Hg2+ in aqueous environment which operate through two different channels, optic/redox and optic/fluorescent, are reported. The optical change in sensing can be used even for a "naked-eye" detection of Hg2+ ions, whereas the fluorescent response can be modulated by varying the solvent polarity.